Is there a desktop app that will alert me when my reputation changes, and when I have a new answer or comment on any of my questions?

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There sure is: StackApplet.

Keep in mind that right now, it is only available for Linux users - but a Windows version is in the works.

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I ve heard the guys at busyfounder.com are preparing an app called busydeveloper that will add github, hackernews and stackoverflow in order to track this kind of data.

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